Predicted secondary structure of isrA Hfq binding RNA
Identifiers
Symbol
isrA
Rfam
RF01385
Other data
RNA type
gene, sRNA
Domain(s)
Enterobacteriaceae
PDB structures
PDBe
Hfq protein from S. aureus with a bound sRNA.
An Hfq binding sRNA is an sRNA that binds the bacterial RNA binding protein called Hfq. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised (see list).
Many of these RNAs share a similar structure composed of three stem-loops.[1] Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium.[2][3][4] A transcriptome wide study on Hfq binding sites in Salmonella mapped 126 Hfq binding sites within sRNAs.[5] Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5′-AAYAAYAA-3′.[6] Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen Erwinia amylovora. 12 of them were confirmed by Northern blot.[7]
^Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003). "Global analysis of small RNA and mRNA targets of Hfq". Mol. Microbiol. 50 (4): 1111–1124. doi:10.1046/j.1365-2958.2003.03734.x. PMID 14622403. S2CID 40056275.
^Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J (December 2007). "A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome". Molecular Microbiology. 66 (5): 1174–1191. doi:10.1111/j.1365-2958.2007.05991.x. PMID 17971080.
^Sittka A, Lucchini S, Papenfort K, et al. (2008). Burkholder WF (ed.). "Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq". PLOS Genetics. 4 (8): e1000163. doi:10.1371/journal.pgen.1000163. PMC 2515195. PMID 18725932.
^Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, et al. (April 2008). "Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence". Nucleic Acids Research. 36 (6): 1913–1927. doi:10.1093/nar/gkn050. PMC 2330248. PMID 18267966.
^Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016). "Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo". EMBO J. 35 (9): 991–1011. doi:10.15252/embj.201593360. PMC 5207318. PMID 27044921.
^Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R (2010). "Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts". Nucleic Acids Res. 38 (11): 3794–3808. doi:10.1093/nar/gkq032. PMC 2887942. PMID 20348540.
^Zeng, Quan; Sundin, George W. (2014-01-01). "Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function". BMC Genomics. 15 (1): 414. doi:10.1186/1471-2164-15-414. ISSN 1471-2164. PMC 4070566. PMID 24885615.
mediated by interacting with Hfq bindingsRNA. In E. coli, Hfq mutants show multiple stress response related phenotypes. The Hfq protein is now known to regulate...
sequencing Hfq-bindingsRNA found that the Watson strand did indeed encode an sRNA. FnrS has been shown to downregulate 32 different mRNAs in Enterobacteria...
Listeria Hfqbinding LhrA is a ncRNA that was identified by screening for RNA molecules which co-immunoprecipitated with the RNA chaperone Hfq. This RNA is...
chaperone protein. Binding of this sRNA to the hfq2 mRNA results in accelerated decay of the mRNA. Bacterial small RNAHfqbindingsRNA Ramos CG, da Costa...
a HfqbindingsRNA. Further evidence has shown that SroB negatively regulates the outer membrane protein YbfM by sequestering the ribosome binding site...
known. However, the RNA-binding protein Hfq is implicated in the process. Hfq binds to rpoS mRNA in vitro and may thereby modify rpoS mRNA structure for optimal...
enterobacterial sRNAs can benefit from transcriptome wide Hfq-binding maps. BSRD (kwanlab.bio.cuhk.edu.hk/BSRD) is a repository for published sRNA sequences...
sometimes require aids from RNA chaperone protein such as Hfq to exert their functions. Due to the complexity of the trans-acting asRNAs, they are currently considered...
SgrS (sugar transport-related sRNA, previously named ryaA) is a 227 nucleotide small RNA that is activated by SgrR in Escherichia coli during glucose-phosphate...
non-coding RNA. It was discovered in genome-wide identification of HfqbindingsRNAs in plant pathogen Erwinia amylovora. Together with Hfq it positively...
new anti-sRNA. A major contributor to this approach is the Hfq protein, a conserved RNA-binding protein that is known to attach various sRNAs. However...
least nine small RNA families in its genome. The small RNA (sRNA) families were identified through RNomics – the direct analysis of RNA molecules isolated...
chaperone Hfq acts to enhance binding of NrrF or stabilizes the NrrF/sdh transcript duplex. Binding of NrrF results in down regulation of the sdhCDAB mRNA transcript...
showed varying expression patterns, many of the newly discovered RNAs were shown to be Hfq-independent and most carried a C-rich motif (UCCC). Represses...
levels could be detected in exponentially growing cells as well. This RNA binds the Hfq protein and regulates levels of gene expression by an antisense mechanism...
mRNA targets. It also protects the unstable molecules from free degradation by RNase. Abundance of Hfq limits qrr RNAbinding, as the separate RNAs compete...
"Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure". RNA. 9 (1): 33–43. doi:10.1261/rna.2570803. PMC 1370368...
2007). "Distinct and overlapping binding sites of Pseudomonas aeruginosa Hfq and RsmA proteins on the non-coding RNA RsmY". Biochemical and Biophysical...
Firstly, to attach sRNA to targeted mRNA a Hfq (chaperone protein) is needed. Once the attachment is done, if the complex Hfq-sRna ends on TIR, it blocks...
most highly expressed in stationary phase. SdsR/RyeB RNA interacts with Hfq. The homologous sRNA in S. enterica was shown to regulate synthesis of major...
protein. ArcZ is an HfqbindingRNA that functions as an antisense regulator of a number of protein coding genes. This non-coding RNA was discovered in...
controlled by quorum sensing, through binding to the RNA chaperone Hfq, then hindering its interaction with the small RNAs that, ultimately, control the production...
X, Wartell RM (2008). "Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNAbinding and the influence of the 5′ rpoS mRNA leader region". Biochemistry. 47...
Hfq is pleiotropic with a variety of interactions, generally associated with translation regulation. These include blocking ribosome binding to mRNA,...
RNA interaction with its target messages. Binding to Hfq alters the conformation of OxyS. The 109 nucleotide RNA is thought to be composed of three stem-loops...
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